水稻叶形及产量相关性状主效QTL的精细定位与功能分析
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摘要
株型改良是提高水稻产量的重要途径之一,适当的叶形和株高对于提升冠层的光合利用率、促进作物增产具有积极的作用。QTL定位是解析水稻复杂农艺性状遗传基础的主要手段之一。前期,我们利用优良籼稻保持系珍汕97和株叶形态优良的强势恢复系93-11为亲本构建回交重组自交系,并对一系列株型性状和产量相关性状进行QTL定位,发现许多一因多效或多基因紧密连锁的QTL区段控制水稻株型和产量相关性状。在此基础上,本研究主要针对位于第一和第8染色体上的两个效应较大的QTL簇进行精细定位和图位克隆,解析水稻株叶形态及产量形成的分子遗传基础,为水稻高产分子育种提供有用的靶基因。主要结果如下：
1.针对第1染色体短臂RM283—RM8083区间上同时控制剑叶长宽、一二次枝梗数和穗重的QTL簇,通过筛选高世代回交群体中重组交换单株,构建覆盖该区段的纯合染色体片段代换系,以及利用后代家系测验的方法缩小和锚定目的基因的位置,将控制剑叶长度的QTL (qFL1)精细定位在约31.3kb的范围内,该区域包含了4个候选基因。条件QTL分析发现,qFL1很可能是一个同时控制叶片大小和产量相关性状的多效性基因。另外,与qFLl紧密连锁的区段还存在一个影响剑叶宽的QTL qFW1.2。说明该区段存在紧密连锁的多基因共同决定叶片的形态和产量构成性状。
2.qFL1区段上两个主要候选基因,成花素同源基因OsFTLl和ABC转运子,在亲本间存在序列差异。比较近等基因系NILZS97和NIL93-11的表达量发现,OsFTLl的表达量在栽后两周和40天的苗期叶片以及抽穗前7天的剑叶中均有极显著的差异,表明OsFTLl最有可能是影响叶片形态和产量相关性状的目的基因。
3.针对第8染色体短臂RM5428—MRG2181区间上同时控制抽穗期、剑叶长宽、株高、叶片间距、穗长、穗抽出度、一二次枝梗数和穗重的QTL簇,我们利用三个杂合自交后代家系(HIFs)对其效应进行了验证和目标区段的缩小。利用新开发的一系列SSR、InDel和测序标记,结合重组交换单株的后代家系测验,将目标QTL精细定位在20kb的范围内,并确定了两个候选基因：CCAAT盒结合蛋白和转运酶蛋白。转基因互补测验显示,CCAAT盒结合蛋白能够不同程度地互补珍汕97遗传背景的近等基因系受体,使抽穗期、株高和产量相关性状同时发生改变；而转运酶蛋白没有产生明显的表型,说明CCAAT盒结合蛋白就是控制多个表型的目标基因,具有一因多效的作用。我们将其命名为Ghd8(Grain number, plant height, and heading date8)。
4.利用HIFs对目标QTL效应区段验证表明,Ghd8效应受背景中其它基因比如qHD6.1和Ghd7的影响。在Ghd7为品种93-11的基因型时,Ghd8区间表现为完全显性；当Ghd7为珍汕97基因型时,Ghd8效应大大减小,说明Ghd7与Ghd8存在遗传互作。
5.Ghd8近等基因系和转基因株系的表达谱分析发现,该基因在全生育期内都有表达,其中在剑叶和根内表达量较高。在短日照条件下,Ghd8具有上调Ehdl、 Hd3a和RFT1表达的作用,促进抽穗；在长日照条件下,Ghd8抑制Ehd1、Hd3a和RFT1的表达,能够延迟抽穗；但在长短日照条件下,Ghd8均不影响节律钟基因OsGI和早开花基因OsMADS50, OsMADS51和RID1表达。表明Ghd8在长短日照条件对Ehd1-Hd3a开花路径具有双向调控的作用。
Improvement of plant morphology is an important approach to increase rice yield. The proper leaf shape and plant height can increase photosynthetic efficiency of rice, which thus is important target for high yield breeding. QTL mapping is one of the main methods for dissection of the genetic base of complex agronomic traits in crops. In a previous study, through using a backcross recominbant inbred lines (BRILs) derived from a cross of93-11and Zhenshan97, both elite indica hybrid rice parents, we found that about7genomic regions on chromosome1,3,6,7,8,11and12showed the pleiotropy, which were controlling the leaf shape and yield traits simultaneously. To deepen our understanding of the molecular and genetic base of the plant morphology, and to provide desirable genes for marker-assisted breeding for improvement of high-yield potential in rice, two QTL clusters each on chromosomes1and8with large effects controlling the leaf shape and yield traits have been targeted for fine mapping and cloning in our study. The main results are present below:
1. To dissect the cluster QTL in the region of RM283—RM8083on the short arm of chromosome1affecting flag leaf length (FL), flag leaf width (FW), primary branch number (PBN), secondary branch number (SBN) and panicle weight (PW), we developed a subset of homologous CSSLs covering the target region, and screened recombinant plants from an advanced backcross population, and employed progeny test for precisely phenotyping the recombinants. The target QTL (qFL1) affecting various traits was narrowed to a31.3kb region that contains four candidate genes. Using conditional QTL analysis, we found that qFL1had a pleiotropic effect on the leaf size and yield related traits; and another minor-effect QTL (qFW1.2) close to qFL1was also detected for flag leaf width. These results suggest that the pleiotropy of qFL1and its closely linked gene affected the leaf size and yield related traits.
2. The comparative expression analysis in leaves of a pariwise of near-isogenic lines (NILs) at three leaf developmental phases, which including the young leaf stage of seedlings, about40days after transplantation, and the mature stage about seven days before heading, shows that two annotated genes, OsFTL1a homolog of florigen FT (Flowering locus T) in Arabidopsis, and ATP-binding cassette (ABC) transporter in the31.3kb region are the most likely candidates for qFLl. Particularly, the expression of OsFTL1at all the three stages differed between the near-isogenic lines that carry the alleles of Zhenshan97and93-11respectively.
3. For the cluster QTL on the short arm of chromosome8affecting heading date (HD), flag leaf length (FL), flag leaf width (FL), plant height (PH), distance between flag leaf and secondary leaf (FD), panicle length (PL), panicle exsertion (PE), primary branch number (PBN), secondary branch number (SBN) and panicle weight (PW), three heterogeneous inbred families (HIFs) with the heterozygous target region in different genetic backgrounds were used to vadidate the QTL effect and to narrow down the target gene. One of three HIFs with large effect at the QTL was used to construct a large segregative population to screen the recombinant plants for fine-mapping. Through developing a set of SSR, InDel and sequencing markers, and progeny testing of the recombinants, a20kb region containing two ORFs (Open Reading Frames) was determined as candidates for the QTL. The two annotated genes are CCAAT-box binding factor and transferase protein. Complemention test showed that CCAAT-box binding factor is that target gene affecting various traits including grains number, heading date and plant height. We thus renamed it Ghd8.
4. The effect magnitudes of Ghd8in the three HIFs depended on the other QTLs in the genetic background, especially qHD6.1and qHD7on chromosomes6and7. When the alleles of qHD7, a QTL corresponding a cloned gene Ghd7, was from93-11, the distribution of heading date in the HIF carrying the alleles of93-11at qHD7showed an obvious segregation of two peaks with the3:1ratio, and the alleles of93-11is complete dominance; but the other two HIFs carrying the alleles of Zhengshan97at qHD7showing normal distribution demonstrated the effect of Ghd8was small. These results indicate that Ghd7might interact with Ghd8.
5. Ghd8was constitutively expressed in different tissues, of which the expression level in flag leaf and root were a little higher than other tissues. Through comparative analysis of the expressive profile of several flowering genes of the photoperiod pathway in the Ghd8positive and negative transgenic plants, we found that Ghd8could up-regulate Ehdl, Hd3a and RFT1, and promote flowering in the short-day conditions, and down-regulate Ehdl, Hd3a and RFT1and delay flowering in the long-day conditions; however, the circadian clock gene OsGI and early flowering gene OsMADS50,OsMADS51and RID1were not altered in both conditions. These results indicate that Ghd8has a dual regulatory function in the Ehd1-Hd3a pathway.
1.针对第1染色体短臂RM283—RM8083区间上同时控制剑叶长宽、一二次枝梗数和穗重的QTL簇,通过筛选高世代回交群体中重组交换单株,构建覆盖该区段的纯合染色体片段代换系,以及利用后代家系测验的方法缩小和锚定目的基因的位置,将控制剑叶长度的QTL (qFL1)精细定位在约31.3kb的范围内,该区域包含了4个候选基因。条件QTL分析发现,qFL1很可能是一个同时控制叶片大小和产量相关性状的多效性基因。另外,与qFLl紧密连锁的区段还存在一个影响剑叶宽的QTL qFW1.2。说明该区段存在紧密连锁的多基因共同决定叶片的形态和产量构成性状。
2.qFL1区段上两个主要候选基因,成花素同源基因OsFTLl和ABC转运子,在亲本间存在序列差异。比较近等基因系NILZS97和NIL93-11的表达量发现,OsFTLl的表达量在栽后两周和40天的苗期叶片以及抽穗前7天的剑叶中均有极显著的差异,表明OsFTLl最有可能是影响叶片形态和产量相关性状的目的基因。
3.针对第8染色体短臂RM5428—MRG2181区间上同时控制抽穗期、剑叶长宽、株高、叶片间距、穗长、穗抽出度、一二次枝梗数和穗重的QTL簇,我们利用三个杂合自交后代家系(HIFs)对其效应进行了验证和目标区段的缩小。利用新开发的一系列SSR、InDel和测序标记,结合重组交换单株的后代家系测验,将目标QTL精细定位在20kb的范围内,并确定了两个候选基因：CCAAT盒结合蛋白和转运酶蛋白。转基因互补测验显示,CCAAT盒结合蛋白能够不同程度地互补珍汕97遗传背景的近等基因系受体,使抽穗期、株高和产量相关性状同时发生改变；而转运酶蛋白没有产生明显的表型,说明CCAAT盒结合蛋白就是控制多个表型的目标基因,具有一因多效的作用。我们将其命名为Ghd8(Grain number, plant height, and heading date8)。
4.利用HIFs对目标QTL效应区段验证表明,Ghd8效应受背景中其它基因比如qHD6.1和Ghd7的影响。在Ghd7为品种93-11的基因型时,Ghd8区间表现为完全显性；当Ghd7为珍汕97基因型时,Ghd8效应大大减小,说明Ghd7与Ghd8存在遗传互作。
5.Ghd8近等基因系和转基因株系的表达谱分析发现,该基因在全生育期内都有表达,其中在剑叶和根内表达量较高。在短日照条件下,Ghd8具有上调Ehdl、 Hd3a和RFT1表达的作用,促进抽穗；在长日照条件下,Ghd8抑制Ehd1、Hd3a和RFT1的表达,能够延迟抽穗；但在长短日照条件下,Ghd8均不影响节律钟基因OsGI和早开花基因OsMADS50, OsMADS51和RID1表达。表明Ghd8在长短日照条件对Ehd1-Hd3a开花路径具有双向调控的作用。
Improvement of plant morphology is an important approach to increase rice yield. The proper leaf shape and plant height can increase photosynthetic efficiency of rice, which thus is important target for high yield breeding. QTL mapping is one of the main methods for dissection of the genetic base of complex agronomic traits in crops. In a previous study, through using a backcross recominbant inbred lines (BRILs) derived from a cross of93-11and Zhenshan97, both elite indica hybrid rice parents, we found that about7genomic regions on chromosome1,3,6,7,8,11and12showed the pleiotropy, which were controlling the leaf shape and yield traits simultaneously. To deepen our understanding of the molecular and genetic base of the plant morphology, and to provide desirable genes for marker-assisted breeding for improvement of high-yield potential in rice, two QTL clusters each on chromosomes1and8with large effects controlling the leaf shape and yield traits have been targeted for fine mapping and cloning in our study. The main results are present below:
1. To dissect the cluster QTL in the region of RM283—RM8083on the short arm of chromosome1affecting flag leaf length (FL), flag leaf width (FW), primary branch number (PBN), secondary branch number (SBN) and panicle weight (PW), we developed a subset of homologous CSSLs covering the target region, and screened recombinant plants from an advanced backcross population, and employed progeny test for precisely phenotyping the recombinants. The target QTL (qFL1) affecting various traits was narrowed to a31.3kb region that contains four candidate genes. Using conditional QTL analysis, we found that qFL1had a pleiotropic effect on the leaf size and yield related traits; and another minor-effect QTL (qFW1.2) close to qFL1was also detected for flag leaf width. These results suggest that the pleiotropy of qFL1and its closely linked gene affected the leaf size and yield related traits.
2. The comparative expression analysis in leaves of a pariwise of near-isogenic lines (NILs) at three leaf developmental phases, which including the young leaf stage of seedlings, about40days after transplantation, and the mature stage about seven days before heading, shows that two annotated genes, OsFTL1a homolog of florigen FT (Flowering locus T) in Arabidopsis, and ATP-binding cassette (ABC) transporter in the31.3kb region are the most likely candidates for qFLl. Particularly, the expression of OsFTL1at all the three stages differed between the near-isogenic lines that carry the alleles of Zhenshan97and93-11respectively.
3. For the cluster QTL on the short arm of chromosome8affecting heading date (HD), flag leaf length (FL), flag leaf width (FL), plant height (PH), distance between flag leaf and secondary leaf (FD), panicle length (PL), panicle exsertion (PE), primary branch number (PBN), secondary branch number (SBN) and panicle weight (PW), three heterogeneous inbred families (HIFs) with the heterozygous target region in different genetic backgrounds were used to vadidate the QTL effect and to narrow down the target gene. One of three HIFs with large effect at the QTL was used to construct a large segregative population to screen the recombinant plants for fine-mapping. Through developing a set of SSR, InDel and sequencing markers, and progeny testing of the recombinants, a20kb region containing two ORFs (Open Reading Frames) was determined as candidates for the QTL. The two annotated genes are CCAAT-box binding factor and transferase protein. Complemention test showed that CCAAT-box binding factor is that target gene affecting various traits including grains number, heading date and plant height. We thus renamed it Ghd8.
4. The effect magnitudes of Ghd8in the three HIFs depended on the other QTLs in the genetic background, especially qHD6.1and qHD7on chromosomes6and7. When the alleles of qHD7, a QTL corresponding a cloned gene Ghd7, was from93-11, the distribution of heading date in the HIF carrying the alleles of93-11at qHD7showed an obvious segregation of two peaks with the3:1ratio, and the alleles of93-11is complete dominance; but the other two HIFs carrying the alleles of Zhengshan97at qHD7showing normal distribution demonstrated the effect of Ghd8was small. These results indicate that Ghd7might interact with Ghd8.
5. Ghd8was constitutively expressed in different tissues, of which the expression level in flag leaf and root were a little higher than other tissues. Through comparative analysis of the expressive profile of several flowering genes of the photoperiod pathway in the Ghd8positive and negative transgenic plants, we found that Ghd8could up-regulate Ehdl, Hd3a and RFT1, and promote flowering in the short-day conditions, and down-regulate Ehdl, Hd3a and RFT1and delay flowering in the long-day conditions; however, the circadian clock gene OsGI and early flowering gene OsMADS50,OsMADS51and RID1were not altered in both conditions. These results indicate that Ghd8has a dual regulatory function in the Ehd1-Hd3a pathway.
引文
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